More than 300 budget airline flights scheduled to travel through French airspace were cancelled on Wednesday as French air traffic controllers continued their industrial action over a planned overhaul of the industry by the European Commission.

Flights between the UK and France were severely affected, with Ryanair cancelling 250 flights and easyJet cancelling 66.

Some 1,800 flights were cancelled on Tuesday as the French controllers began a two-day strike in protest at plans to centralise operations across the EU to avoid duplication in the 27 member states.

EasyJet said it had had to cancel 128 flights on Tuesday to and from airports including Charles de Gaulle, Orly, Lyon, Nice, Marseille, Toulouse and Bordeaux, adding that a further 66 had already been cancelled on Wednesday.

“There have been 66 cancellations of flights to and from the UK as a result of the strike action,” said a spokeswoman. “We have notified passengers affected by email and text but recommend that passengers travelling today keep a close eye on our website, which is being updated regularly.”

Ryanair, which described the strike as “grossly unfair”, also urged passengers to monitor its website.

“Ryanair was forced to cancel over 200 flights on Tuesday as this unwarranted strike action not only affected flights to and from France, but also flights travelling through French airspace,” said a spokesman.

“Regrettably, we have had to cancel a further 250 flights on Wednesday and we sincerely apologise to passengers, but the circumstances are entirely beyond our control.”

A spokesman for British Airways said that although it had been forced to cancel a small number of flights on Tuesday, it had not been as badly affected as some airlines.

The UK travel organisation Abta also criticised the industrial action.

“We always think it is deeply regrettable turn to strike action as their first option in negotiations,” said a spokesman. “It penalises holidaymakers.”

He added that passengers whose flights were cancelled would be entitled to a refund or a replacement flight and should contact their airline.

The European Transport Workers’ Federation has called days of industrial action – including strikes, protests and walk-outs by union members across the European Union – to make plain its opposition to what it terms “a never-ending process of liberalisation, deregulation and cost cutting”.